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United States Department of Agriculture

Agricultural Research Service

Research Project: DOMESTIC, EXOTIC, AND EMERGING DISEASES OF CITRUS, VEGETABLES, AND ORNAMENTALS (DEED) Title: Evolving diversity of ‘Candidatus Liberibacter asiaticus’ revealed by comparative analysis of two related intragenic tandem repeat genes

Authors
item Zhou, Lijuan -
item Powell, Charles -
item Li, Wenbin -
item Hoffman, Michele
item Fan, Guocheng -
item Liu, Bo -
item Lin, Hong
item Duan, Ping

Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 15, 2011
Publication Date: July 22, 2011
Citation: Zhou, L., Powell, C., Li, W., Hoffman, M.T., Fan, G., Liu, B., Lin, H., Duan, Y. 2011. Evolving diversity of ‘Candidatus Liberibacter asiaticus’ revealed by comparative analysis of two related intragenic tandem repeat genes. Applied and Environmental Microbiology. 77:18.

Interpretive Summary: Citrus huanglongbing (HLB) is an extremely damaging citrus disease throughout the world. Citrus HLB bacterium, ‘Candidatus Liberibacter asiaticus’ (Las) is only species found in Florida and the most prevalent species of Liberibacter worldwide. This fastidious bacterium is sieve cell-restricted and transmitted by the Asian citrus psyllid (Diaphorina citri). Different types of symptoms and different bacterial titers were observed in HLB-affected citrus and periwinkle plants. Although the disease is century-old, little is known about the genetic diversity of Las and possible strain variations. The complete genome sequence Las Psy62 provides wealth of information for genetic diversity and evolution study on Las bacterium. During the gap closing process for the Las genome, two related and hyper variable genes (hyvI and hyvII) were identified in the prophage regions of the psy62 Las genome. Like the pathogenicity gene, pthA of citrus canker bacterium (Xanthomonas citri), the hyvI contains 12 nearly identical 132-bp tandem repeats and 4 partial repeats. Frequent deletions or insertions of these repeats within the hyvI/II genes were observed, but none of which disrupted the open reading frame. Sequence analysis of the hyvI/hyvII genes from 35 Las DNA samples collected globally revealed sequence conservation within the individual repeats but an extensive variation regarding repeat numbers, their rearrangement, and the sequences outside of repeat region. Phylogenetic analysis of these isolates indicated a strong potential of multiple populations existed in the Las bacteria in the world, and a multi-source introduction of the Las bacterium into Florida. Functional studies of these genes may provide more useful information regarding their role in disease development or insect transmission.

Technical Abstract: ‘Candidatus Liberibacter asiaticus’ (Las) is the most prevalent species of the citrus Huanglongbing bacteria. Two related and hyper variable genes (hyvI and hyvII) were identified in the prophage regions of the psy62 Las genome. The hyvI (2760 bp) contains 12 nearly identical 132-bp repeats and 4 partial repeats while the hyvII (1026 bp) contains only one incomplete repeat and shares homology with hyvI. Frequent deletions or insertions of these repeats within the hyvI/II genes were observed, but none of which disrupted the open reading frame. Sequencing analysis of the hyvI/hyvII genes from 35 Las DNA samples collected globally revealed sequence conservation within the individual repeats but an extensive variation regarding repeat numbers, their rearrangement, and the sequences outside of repeat region. These differences are found not only in samples with distinct geographical origins but also from a single origin and even from a single Las-infected sample. The Florida isolates contain both hyvI and hyvII while all other global isolates contain only one of the two. Interclade assignments of the putative HyvI/II proteins from Florida isolates with other global isolates in the phylogenic trees imply a strong potential of multiple populations existed in the Las bacteria in the world, and a multi-source introduction of the Las bacterium into Florida. On the other hand, high copy number of these multiple nearly-identical repeats provides a significant advantage for developing more sensitive diagnosis tools.

Last Modified: 10/24/2014
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